I used to work for them, it will still go to court even if you set up a payment plan at this stage.
The reason being, is because you have already defaulted more than once on the existing payment plan. You have to have done to receive the court summons.
The key word in all of this is tax so the court order grants the council further power to recover the monies owed. This includes attachment to earnings (taken directly from a salary from your employer) or in the case of self employed people they can bailiff your property.
Legally it is a 10 month payment plan with the council each time you get the new bill payments running from 1st April and the final one on 1st January. It is at the discretion of the council to extend this into a 12 month payment plan.
The good news is you have been paying, all along, maybe not the right amount at the right time but you have. And you have been in contact with them all the way through.
There is a huge difference between people who won't pay and then you, people who can't pay. We would bend over backwards to accommodate someone like you. We never judged those who couldn't pay. If you think the council tax workers were on good money you would be wrong 
We were a tiny council and ran thousands of these through the court each time. You are not alone. Ring up, do not worry. Explain when you can make a payment. But it will still go through the court for a "liability order."
You don't need to go to court, all it is is a large pile of papers that the judge stamps to say you are the people liable for the council tax and that should you not pay the council can take it further.
Just remember, this all starts again in April.
Good luck. Hope you read this before your phone call.